Research workbench
High resolution structure of human arginase I in complex with the strong inhibitor N(OMEGA)-hydroxy-nor-L-arginine (nor-noha)
Analyse High resolution structure of human arginase I in complex with the strong… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KV2
- Type
- protein
- Length
- 626 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arginase-1
- EC
- 3.5.3.1
- UniProt
- P05089
- Ligands
- NNH, MN
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Arginase-1 (EC 3.5.3.1) | protein | 313 | 43% helix, 17% strand | P05089 |
Ligands and binding sites
- NNH · Nor-N-omega-hydroxy-L-arginine · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1014 | 0.77 | 0.79 | 93 | NNH |
| 2 | 80 | 0.41 | 0.80 | 20 | NNH |
| 3 | 54 | 0.36 | 0.79 | 14 | empty |
| 4 | 56 | 0.32 | 0.76 | 13 | empty |
| 5 | 61 | 0.29 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 471 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3KV2 · HIGH RESOLUTION STRUCTURE OF HUMAN ARGINASE I IN COMPLEX WITH THE STRONG INHIBITOR… · the same entry in another collection · chain B against B, TM-score 1.00
- P05089 · AlphaFold monomer V2.0 prediction for arginase-1 (P05089) · a predicted model of the same protein · chain B against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P05089
- Elsewhere: RCSB PDB 3KV2 · PDBe 3KV2 · UniProt P05089
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